Sample preparation on a solid support

ABSTRACT

Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5′-tagged double-stranded target DNA on a surface. The methods are useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.14/671,071 filed Mar. 27, 2015, (published as US-2015-0284714-A1), whichis a continuation of U.S. application Ser. No. 13/790,220, filed Mar. 8,2013 (now U.S. Pat. No. 9,683,230), which claims the benefit of U.S.Provisional Application No. 61/750,682, filed on Jan. 9, 2013, thecontents of each of which are herein expressly incorporated by referencefor all purposes.

BACKGROUND

There are a variety of methods and applications for which it isdesirable to generate a library of fragmented and tagged DNA moleculesfrom double-stranded DNA (dsDNA) target molecules. Often, the purpose isto generate smaller DNA molecules (e.g., DNA fragments) from largerdsDNA molecules for use as templates in DNA sequencing reactions.

Many of the methods currently used for fragmentation and tagging ofdouble-stranded DNA for use in next-generation sequencing are wastefulof the DNA, require expensive instruments for fragmentation, and theprocedures for fragmentation, tagging and recovering tagged DNAfragments are difficult, tedious, laborious, time-consuming,inefficient, costly, require relatively large amounts of sample nucleicacids. In addition, many of these methods generate tagged DNA fragmentsthat are not fully representative of the sequences contained in thesample nucleic acids from which they were generated. Thus, what isneeded in the art are methods that provide speed and ease of use whengenerating libraries of tagged DNA fragments from target DNA and whichcan be easily applied to nucleic acid analysis methods such asnext-generation sequencing and amplification methods.

BRIEF SUMMARY

Presented herein are methods and compositions for nucleic acid samplepreparation on a solid support. The methods and compositions especiallyrelate to methods and compositions for fragmenting and tagging DNA usingtransposon compositions immobilized to a solid support. The methods andcompositions presented herein are useful, for example, for generatinglibraries of tagged DNA fragments for use, e.g., in next generationsequencing methods, and the like. In some preferred embodiments, thepresent invention relates to preparation of linear ssDNA fragments on asolid support from target DNA comprising any dsDNA of interest(including double-stranded cDNA prepared from RNA), from any source, forgenomic, subgenomic, transcriptomic, or metagenomic analysis, oranalysis of RNA expression.

Accordingly, presented herein are methods of preparing an immobilizedlibrary of tagged DNA fragments comprising: (a) providing a solidsupport having transposome complexes immobilized thereon, wherein thetransposome complexes comprise a transposase bound to a firstpolynucleotide, the first polynucleotide comprising (i) a 3′ portioncomprising a transposon end sequence, and (ii) a first tag comprising afirst tag domain; and (b) applying a target DNA to the solid supportunder conditions whereby the target DNA is fragmented by the transposomecomplexes, and the 3′ transposon end sequence of the firstpolynucleotide is transferred to a 5′ end of at least one strand of thefragments; thereby producing an immobilized library of double-strandedfragments wherein at least one strand is 5′-tagged with the first tag.In some embodiments, the transposome complexes comprise a secondpolynucleotide comprising a region complementary to said transposon endsequence. The methods can further comprise (c) providing transposomecomplexes in solution and contacting the transposome complexes with theimmobilized fragments under conditions whereby the target DNA isfragmented by the transposome complexes in solution; thereby obtainingimmobilized nucleic acid fragments having one end in solution. In someembodiments, the transposome complexes in solution can comprise a secondtag, such that the method generates immobilized nucleic acid fragmentshaving a second tag, the second tag in solution. The first and secondtags can be different or the same.

Also presented herein are solid supports having a library of tagged DNAfragments immobilized thereon prepared according to the above methods orother methods. For example, presented herein are solid supports havingtransposome complexes immobilized thereon, wherein the transposomecomplexes comprise a transposase bound to a first polynucleotide, thepolynucleotide comprising (i) a 3′ portion comprising a transposon endsequence, and (ii) a first tag comprising a first tag domain.

Also presented herein are methods of generating a flowcell, comprisingimmobilizing a plurality of transposome complexes to a solid support,the transposome complexes comprising a transposase bound to a firstpolynucleotide, the first polynucleotide comprising (i) a 3′ portioncomprising a transposon end sequence, and (ii) a first tag comprising afirst tag domain.

The methods can further comprise providing a solid support having aplurality the first polynucleotides immobilized thereon, and contactingthe solid support with transposase holoenzyme and a secondpolynucleotide, the second polynucleotide comprising a regioncomplementary to the transposon end sequence. In some embodiments of themethods, immobilizing comprises (a) providing a solid support havingamplification primers coupled thereto; (b) hybridizing a secondpolynucleotide to one of the amplification primers, the secondoligonucleotide comprising a region complementary to a transposon endsequence and a region complementary to the first tag; (c) extending theamplification primer using a polymerase to generate a duplex comprisingthe first polynucleotide hybridized to the second polynucleotide, thefirst polynucleotide immobilized directly to the solid support; and (d)contacting the solid support with transposase holoenzyme, therebyassembling a transposome complex on the solid support.

Also presented herein is a population of microparticles havingtransposome complexes immobilized thereto, the transposome complexescomprising a transposase bound to a first polynucleotide and a secondpolynucleotide; wherein the first polynucleotide is immobilized at its5′ end to the surface of the microparticle and the second polynucleotideis hybridized to the 3′ end of the first polynucleotide; and wherein thefirst polynucleotide comprises: (i) a 3′ portion comprising a transposonend sequence, and (ii) a first tag comprising a first tag domain. Alsopresented herein are methods of producing an immobilized library oftagged DNA fragments comprising contacting a target DNA with the abovepopulation of microparticles to generate immobilized tagged DNAfragments.

Also presented herein are methods of generating a library of tagged DNAfragments for index-directed assembly into a longer sequence read, themethod comprising: providing a population of microparticles havingtransposome complexes immobilized thereto, the transposome complexescomprising a transposase bound to a first polynucleotide comprising anindex domain associated with the microparticle and a secondpolynucleotide; applying a target DNA to the population ofmicroparticles, thereby generating immobilized DNA fragments that aretagged with the index domain. In certain embodiments of the abovemethods, the first polynucleotide is immobilized at its 5′ end to thesurface of the microparticle and the second polynucleotide is hybridizedto the 3′ end of the first polynucleotide; and wherein the firstpolynucleotide comprises: (i) a 3′ portion comprising a transposon endsequence, and (ii) the index domain; and wherein the population ofmicroparticles comprises at least a plurality of index domains, andwherein the first polynucleotides on an individual microparticle sharethe same index domain.

Also presented herein is a method for sequencing a plurality of targetDNA molecules, comprising: applying a plurality of target DNA to a solidsupport having transposome complexes immobilized thereon underconditions whereby the target DNA is fragmented by the transposomecomplexes; thereby producing an immobilized library of double-strandedfragments, wherein a first portion of each target DNA is attached tosaid solid support at a first location on said solid support and asecond portion of each target DNA is attached to said solid support at asecond location on said solid support; and mapping said immobilizedlibrary of double-stranded fragments to generate a set of locations thatare linked by each target DNA; determining the sequences of said firstand second portions of the target DNA; and correlating said set oflocations to determine which first and second portions are linked bysaid target DNA and to determine the sequence of the target DNAmolecules.

In some embodiments of the methods and compositions presented herein,the transposome complexes are present on the solid support at a densityof at least 10³, 10⁴, 10⁵, 10⁶ complexes per mm². In some embodiments,the transposome complex comprises a hyperactive transposase, such as Tn5transposase.

In some embodiments of the methods and compositions presented herein,the tag domain can comprise, for example, a region for clusteramplification. In some embodiments, the tag domain can comprise a regionfor priming a sequencing reaction.

In some embodiments of the methods and compositions presented herein,the solid support can comprise, for example, microparticles, a patternedsurface, wells and the like. In some embodiments, the transposomecomplexes are randomly distributed upon the solid support. In someembodiments, the transposome complexes are distributed on a patternedsurface.

The details of one or more embodiments are set forth in the accompanyingdrawings and the description below. Other features, objects, andadvantages will be apparent from the description and drawings, and fromthe claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1a and 1b show the general concept according to one embodiment.

FIG. 2a is a schematic illustrating a tagmentation reaction. FIG. 2b isa schematic with the resulting bridge redrawn to clarify the nature ofthe resulting bridge.

FIGS. 3a and 3b illustrate an embodiment where two forms of transposomeare assembled on the surface of a flowcell. Addition of DNA to theflowcell results in tagmentation and coupling of the DNA to thetransposomes. Also shown in FIG. 3a are different types of resultingclusters: P7:P7, P5:P5, and P5:P7 clusters.

FIGS. 4a and 4b illustrate another embodiment. In FIG. 4a , only oneform of surface bound transposome (e.g. P5 transposome) is present,resulting in bridges having the same tag sequence at each end.Additional transposomes are added to further fragment the bridgestructures and incorporate an additional tag sequence (P7). FIG. 4bshows amplification to generate pairs of clusters resulting from eachtransposome stump which represent two adjacent fragments in the originalintact DNA sample (FIG. 4b ).

FIGS. 5a, 5b, 5c and 5d illustrate different methods for assemblingsurface bound transposome complexes.

FIGS. 6a and 6b set forth the design for an experiment set forth asExample 1.

FIG. 7 sets forth representative data obtained in an experimentconducted according to the design set forth in Example 1.

FIG. 8 sets forth representative data obtained in an experimentconducted according to the design set forth in Example 1.

FIGS. 9-12 are illustrations of assembly of bead-bound transposomes andsubsequent tagmentation according to one embodiment.

FIG. 13 is an illustration of surface bound transposomes according toone embodiment.

FIG. 14 is an illustration of tagmentation performed on bead-boundtransposomes according to one embodiment.

FIG. 15 is an illustration of tagmentation and barcoding ofsub-fragments performed on bead-bound transposomes according to oneembodiment.

FIG. 16 is an illustration of tagmentation and barcoding ofsub-fragments performed on bead-bound transposomes according to oneembodiment.

FIG. 17 shows an exemplary scheme of how to avoid producing a populationof clusters that contain sequences that do not align to the targetgenomic DNA.

FIGS. 18a-18b provide more information on surface tagmentation. FIG. 18ashows an exemplary scheme of assembling transposomes on a surface andusing in a surface tagmentation reaction. FIG. 18b shows the results ofusing surface tagmentation reaction with results indicating an increasein the percentage of clusters that aligned to target E. coli sequence.

DETAILED DESCRIPTION

Current protocols for sequencing nucleic acid samples routinely employ asample preparation process that converts DNA or RNA into a library oftemplates. These methods can result in loss of DNA sample and oftenrequire expensive instruments for fragmentation. In addition, the samplepreparation methods are often difficult, tedious, and inefficient.

In standard sample preparation methods, each template contains anadaptor at either end of the insert and often a number of steps arerequired to both modify the DNA or RNA and to purify the desiredproducts of the modification reactions. These steps are performed insolution prior to the addition of the adapted fragments to a flowcellwhere they are coupled to the surface by a primer extension reactionthat copies the hybridized fragment onto the end of a primer covalentlyattached to the surface. These ‘seeding’ templates then give rise tomonoclonal clusters of copied templates through several cycles ofamplification.

The number of steps required to transform DNA into adaptor-modifiedtemplates in solution ready for cluster formation and sequencing can beminimized by the use of transposase mediated fragmentation and tagging.This process, referred to herein as ‘tagmentation,’ often involves themodification of DNA by a transposome complex comprising transposaseenzyme complexed with adaptors comprising transposon end sequence.Tagmentation results in the simultaneous fragmentation of the DNA andligation of the adaptors to the 5′ ends of both strands of duplexfragments. Following a purification step to remove the transposaseenzyme, additional sequences are added to the ends of the adaptedfragments by PCR.

Solution-based tagmentation has drawbacks and requires severallabor-intensive steps. Additionally, bias can be introduced during PCRamplification steps. The methods and compositions presented hereinovercome those drawbacks and allow unbiased sample preparation, clusterformation and sequencing to occur on a single solid support with minimalrequirements for sample manipulation or transfer.

The present disclosure relates to the surprising discovery thattransposome complexes pre-coupled to the surface of a flowcell caneffectively fragment, tag and immobilize intact DNA within the flowcell.In specific embodiments, one or more of the strands that comprise thetransposome adaptors are attached to the surface of the flowcell viatheir 5′ end. When intact DNA is pumped onto the flowcell, thetagmentation reaction occurs in the same manner as occurs insolution-based tagmentation reactions, but the resulting productfragments are physically attached to the surface of the flowcell bytheir ends. The transposome adaptor sequences can contain sequences thatenable subsequent cluster generation and sequencing.

The methods and compositions presented herein provide several advantagesover solution-based tagmentation methods. For example, purified,partially purified or even unpurified intact DNA template can be loadeddirectly onto a flowcell for generation of clusters, without priorsample preparation. In addition, the contiguity of sequence informationin the original intact DNA can be physically preserved by thejuxtaposition of tagmented fragments on the surface of the flowcell. Asa further advantage, DNA is physically linked to the surface of theflowcell so purification of reagents following further manipulation ofthe DNA can be achieved by flow-through buffer exchange in the flowcellchannel.

Tagmentation on a Solid Support

In accordance with the above, presented herein are methods of preparingan immobilized library of tagged DNA fragments. In some embodiments, themethods can comprise: (a) providing a solid support having transposomecomplexes immobilized thereon, wherein the transposome complexescomprise a transposase bound to a first polynucleotide, the firstpolynucleotide comprising (i) a 3′ portion comprising a transposon endsequence, and (ii) a first tag comprising a first tag domain; and (b)applying a target DNA to the solid support under conditions whereby thetarget DNA is fragmented by the transposome complexes, and the 3′transposon end sequence of the first polynucleotide is transferred to a5′ end of at least one strand of the fragments; thereby producing animmobilized library of double-stranded fragments wherein at least onestrand is 5′-tagged with the first tag.

As used herein, the term “transposome complex” refers generally to atransposase enzyme non-covalently bound to a double stranded nucleicacid. For example, the complex can be a transposase enzyme preincubatedwith double-stranded transposon DNA under conditions that supportnon-covalent complex formation. Double-stranded transposon DNA caninclude, without limitation, Tn5 DNA, a portion of Tn5 DNA, a transposonend composition, a mixture of transposon end compositions or otherdouble-stranded DNAs capable of interacting with a transposase such asthe hyperactive Tn5 transposase.

A “transposase” means an enzyme that is capable of forming a functionalcomplex with a transposon end-containing composition (e.g., transposons,transposon ends, transposon end compositions) and catalyzing insertionor transposition of the transposon end-containing composition into thedouble-stranded target DNA with which it is incubated, for example, inan in vitro transposition reaction. A transposase as presented hereincan also include integrases from retrotransposons and retroviruses.Transposases, transposomes and transposome complexes are generally knownto those of skill in the art, as exemplified by the disclosure of US2010/0120098, the content of which is incorporated herein by referencein its entirety. Although many embodiments described herein refer to Tn5transposase and/or hyperactive Tn5 transposase, it will be appreciatedthat any transposition system that is capable of inserting a transposonend with sufficient efficiency to 5′-tag and fragment a target DNA forits intended purpose can be used in the present invention. In particularembodiments, a preferred transposition system is capable of insertingthe transposon end in a random or in an almost random manner to 5′-tagand fragment the target DNA.

The term “transposon end” refers to a double-stranded nucleic acid DNAthat exhibits only the nucleotide sequences (the “transposon endsequences”) that are necessary to form the complex with the transposaseor integrase enzyme that is functional in an in vitro transpositionreaction. In some embodiments, a transposon end is capable of forming afunctional complex with the transposase in a transposition reaction. Asnon-limiting examples, transposon ends can include the 19-bp outer end(“OE”) transposon end, inner end (“IE”) transposon end, or “mosaic end”(“ME”) transposon end recognized by a wild-type or mutant Tn5transposase, or the R1 and R2 transposon end as set forth in thedisclosure of US 2010/0120098, the content of which is incorporatedherein by reference in its entirety. Transposon ends can comprise anynucleic acid or nucleic acid analogue suitable for forming a functionalcomplex with the transposase or integrase enzyme in an in vitrotransposition reaction. For example, the transposon end can compriseDNA, RNA, modified bases, non-natural bases, modified backbone, and cancomprise nicks in one or both strands. Although the term “DNA” is usedthroughout the present disclosure in connection with the composition oftransposon ends, it should be understood that any suitable nucleic acidor nucleic acid analogue can be utilized in a transposon end.

The term “transferred strand” refers to the transferred portion of bothtransposon ends. Similarly, the term “non-transferred strand” refers tothe non-transferred portion of both “transposon ends.” The 3′-end of atransferred strand is joined or transferred to target DNA in an in vitrotransposition reaction. The non-transferred strand, which exhibits atransposon end sequence that is complementary to the transferredtransposon end sequence, is not joined or transferred to the target DNAin an in vitro transposition reaction.

In some embodiments, the transferred strand and non-transferred strandare covalently joined. For example, in some embodiments, the transferredand non-transferred strand sequences are provided on a singleoligonucleotide, e.g., in a hairpin configuration. As such, although thefree end of the non-transferred strand is not joined to the target DNAdirectly by the transposition reaction, the non-transferred strandbecomes attached to the DNA fragment indirectly, because thenon-transferred strand is linked to the transferred strand by the loopof the hairpin structure. Additional examples of transposome structureand methods of preparing and using transposomes can be found in thedisclosure of US 2010/0120098, the content of which is incorporatedherein by reference in its entirety.

The terms “tag” and “tag domain” as used herein refer to a portion ordomain of a polynucleotide that exhibits a sequence for a desiredintended purpose or application. Some embodiments presented hereininclude a transposome complex comprising a polynucleotide having a 3′portion comprising a transposon end sequence, and tag comprising a tagdomain. Tag domains can comprise any sequence provided for any desiredpurpose. For example, in some embodiments, a tag domain comprises one ormore restriction endonuclease recognition sites. In some embodiments, atag domain comprises one or more regions suitable for hybridization witha primer for a cluster amplification reaction. In some embodiments, atag domain comprises one or more regions suitable for hybridization witha primer for a sequencing reaction. It will be appreciated that anyother suitable feature can be incorporated into a tag domain. In someembodiments, the tag domain comprises a sequence having a length between5 and 200 bp. In some embodiments, the tag domain comprises a sequencehaving a length between 10 and 100 bp. In some embodiments, the tagdomain comprises a sequence having a length between 20 and 50 bp. Insome embodiments, the tag domain comprises a sequence having a lengthbetween 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150 and200 bp.

In the methods and compositions presented herein, transposome complexesare immobilized to the solid support. In some embodiments, thetransposome complexes are immobilized to the support via one or morepolynucleotides, such as a polynucleotide comprising a transposon endsequence. In some embodiments, the transposome complex may beimmobilized via a linker molecule coupling the transposase enzyme to thesolid support. In some embodiments, both the transposase enzyme and thepolynucleotide are immobilized to the solid support. When referring toimmobilization of molecules (e.g. nucleic acids) to a solid support, theterms “immobilized” and “attached” are used interchangeably herein andboth terms are intended to encompass direct or indirect, covalent ornon-covalent attachment, unless indicated otherwise, either explicitlyor by context. In certain embodiments of the invention covalentattachment may be preferred, but generally all that is required is thatthe molecules (e.g. nucleic acids) remain immobilized or attached to thesupport under the conditions in which it is intended to use the support,for example in applications requiring nucleic acid amplification and/orsequencing.

Certain embodiments of the invention may make use of solid supportscomprised of an inert substrate or matrix (e.g. glass slides, polymerbeads etc.) which has been functionalized, for example by application ofa layer or coating of an intermediate material comprising reactivegroups which permit covalent attachment to biomolecules, such aspolynucleotides. Examples of such supports include, but are not limitedto, polyacrylamide hydrogels supported on an inert substrate such asglass, particularly polyacrylamide hydrogels as described in WO2005/065814 and US 2008/0280773, the contents of which are incorporatedherein in their entirety by reference. In such embodiments, thebiomolecules (e.g. polynucleotides) may be directly covalently attachedto the intermediate material (e.g. the hydrogel) but the intermediatematerial may itself be non-covalently attached to the substrate ormatrix (e.g. the glass substrate). The term “covalent attachment to asolid support” is to be interpreted accordingly as encompassing thistype of arrangement.

The terms “solid surface,” “solid support” and other grammaticalequivalents herein refer to any material that is appropriate for or canbe modified to be appropriate for the attachment of the transposomecomplexes. As will be appreciated by those in the art, the number ofpossible substrates is very large. Possible substrates include, but arenot limited to, glass and modified or functionalized glass, plastics(including acrylics, polystyrene and copolymers of styrene and othermaterials, polypropylene, polyethylene, polybutylene, polyurethanes,Teflon™, etc.), polysaccharides, nylon or nitrocellulose, ceramics,resins, silica or silica-based materials including silicon and modifiedsilicon, carbon, metals, inorganic glasses, plastics, optical fiberbundles, and a variety of other polymers. Particularly useful solidsupports and solid surfaces for some embodiments are located within aflow cell apparatus. Exemplary flow cells are set forth in furtherdetail below.

In some embodiments, the solid support comprises a patterned surfacesuitable for immobilization of transposome complexes in an orderedpattern. A “patterned surface” refers to an arrangement of differentregions in or on an exposed layer of a solid support. For example, oneor more of the regions can be features where one or more transposomecomplexes are present. The features can be separated by interstitialregions where transposome complexes are not present. In someembodiments, the pattern can be an x-y format of features that are inrows and columns. In some embodiments, the pattern can be a repeatingarrangement of features and/or interstitial regions. In someembodiments, the pattern can be a random arrangement of features and/orinterstitial regions. In some embodiments, the transposome complexes arerandomly distributed upon the solid support. In some embodiments, thetransposome complexes are distributed on a patterned surface. Exemplarypatterned surfaces that can be used in the methods and compositions setforth herein are described in U.S. Ser. No. 13/661,524 or US Pat. App.Publ. No. 2012/0316086 A1, each of which is incorporated herein byreference.

In some embodiments, the solid support comprises an array of wells ordepressions in a surface. This may be fabricated as is generally knownin the art using a variety of techniques, including, but not limited to,photolithography, stamping techniques, molding techniques andmicroetching techniques. As will be appreciated by those in the art, thetechnique used will depend on the composition and shape of the arraysubstrate.

The composition and geometry of the solid support can vary with its use.In some embodiments, the solid support is a planar structure such as aslide, chip, microchip and/or array. As such, the surface of a substratecan be in the form of a planar layer. In some embodiments, the solidsupport comprises one or more surfaces of a flowcell. The term“flowcell” as used herein refers to a chamber comprising a solid surfaceacross which one or more fluid reagents can be flowed. Examples offlowcells and related fluidic systems and detection platforms that canbe readily used in the methods of the present disclosure are described,for example, in Bentley et al., Nature 456:53-59 (2008), WO 04/018497;U.S. Pat. No. 7,057,026; WO 91/06678; WO 07/123744; U.S. Pat. Nos.7,329,492; 7,211,414; 7,315,019; 7,405,281, and US 2008/0108082, each ofwhich is incorporated herein by reference.

In some embodiments, the solid support or its surface is non-planar,such as the inner or outer surface of a tube or vessel. In someembodiments, the solid support comprises microspheres or beads. By“microspheres” or “beads” or “particles” or grammatical equivalentsherein is meant small discrete particles. Suitable bead compositionsinclude, but are not limited to, plastics, ceramics, glass, polystyrene,methylstyrene, acrylic polymers, paramagnetic materials, thoria sol,carbon graphite, titanium dioxide, latex or cross-linked dextrans suchas Sepharose, cellulose, nylon, cross-linked micelles and teflon, aswell as any other materials outlined herein for solid supports may allbe used. “Microsphere Detection Guide” from Bangs Laboratories, FishersInd. is a helpful guide. In certain embodiments, the microspheres aremagnetic microspheres or beads.

The beads need not be spherical; irregular particles may be used.Alternatively or additionally, the beads may be porous. The bead sizesrange from nanometers, i.e. 100 nm, to millimeters, i.e. 1 mm, withbeads from about 0.2 micron to about 200 microns being preferred, andfrom about 0.5 to about 5 micron being particularly preferred, althoughin some embodiments smaller or larger beads may be used.

FIGS. 1a and 1b generally illustrate the method according to oneembodiment. A solid support coated with grafted oligonucleotides isshown, some of which contain the ME sequences, will form activetransposome complexes that are physically coupled to the solid supportin the presence of Tn5. The density of these surface bound transposomescan be modulated by varying the density of the grafted oligonucleotidescontaining the ME sequence or by the amount of transposase added to thesolid support. For example, in some embodiments, the transposomecomplexes are present on the solid support at a density of at least 10³,10⁴, 10⁵, or at least 10⁶ complexes per mm².

When double stranded DNA is added to the solid support, the transposomecomplexes will tagment added DNA, thus generating ds fragments coupledat both ends to the surface. In some embodiments, the length of bridgedfragments can be varied by changing the density of the transposomecomplexes on the surface. In certain embodiments, the length of theresulting bridged fragments is less than 100 bp, 200 bp, 300 bp, 400 bp,500 bp, 600 bp, 700 bp, 800 bp, 900 bp, 1000 bp, 1100 bp, 1200 bp, 1300bp, 1400 bp, 1500 bp, 1600 bp, 1700 bp, 1800 bp, 1900 bp, 2000 bp, 2100bp, 2200 bp, 2300 bp, 2400 bp, 2500 bp, 2600 bp, 2700 bp, 2800 bp, 2900bp, 3000 bp, 3100 bp, 3200 bp, 3300 bp, 3400 bp, 3500 bp, 3600 bp, 3700bp, 3800 bp, 3900 bp, 4000 bp, 4100 bp, 4200 bp, 4300 bp, 4400 bp, 4500bp, 4600 bp, 4700 bp, 4800 bp, 4900 bp, 5000 bp, 10000 bp, 30000 bp orless than 100,000 bp. In such embodiments, the bridged fragments canthen be amplified into clusters using standard cluster chemistry, asexemplified by the disclosure of U.S. Pat. Nos. 7,985,565 and 7,115,400,the contents of each of which is incorporated herein by reference in itsentirety.

In some embodiments, the length of the templates is longer than what canbe suitably amplified using standard cluster chemistry. For example, insome embodiments, the length of templates is longer than 100 bp, 200 bp,300 bp, 400 bp, 500 bp, 600 bp, 700 bp, 800 bp, 900 bp, 1000 bp, 1100bp, 1200 bp, 1300 bp, 1400 bp, 1500 bp, 1600 bp, 1700 bp, 1800 bp, 1900bp, 2000 bp, 2100 bp, 2200 bp, 2300 bp, 2400 bp, 2500 bp, 2600 bp, 2700bp, 2800 bp, 2900 bp, 3000 bp, 3100 bp, 3200 bp, 3300 bp, 3400 bp, 3500bp, 3600 bp, 3700 bp, 3800 bp, 3900 bp, 4000 bp, 4100 bp, 4200 bp, 4300bp, 4400 bp, 4500 bp, 4600 bp, 4700 bp, 4800 bp, 4900 bp, 5000 bp, 10000bp, 30000 bp or longer than 100,000 bp. In such embodiments, then asecond tagmentation reaction can be performed by adding transposomesfrom solution that further fragment the bridges, as illustrated, forexample, in FIG. 4a . The second tagmentation reaction can thus removethe internal span of the bridges, leaving short stumps anchored to thesurface that can converted into clusters ready for further sequencingsteps. In particular embodiments, the length of the template can bewithin a range defined by an upper and lower limit selected from thoseexemplified above.

In certain embodiments, prior to cluster generation, the DNA immobilizedby surface tagmentation can imaged. For example, the immobilized DNA canbe stained with an interchelating dye and imaged to preserve a record ofthe position of the backbone of the DNA molecule on the surface.Following cluster generation and sequencing, the coordinates of clusterscan be associated with their position on the original backbone, thusassisting in alignment of reads along a molecule and genome assembly.

In some embodiments, the step of applying a target DNA comprises addinga biological sample to said solid support. The biological sample can beany type that comprises DNA and which can be deposited onto the solidsurface for tagmentation. For example, the sample can comprise DNA in avariety of states of purification, including purified DNA. However, thesample need not be completely purified, and can comprise, for example,DNA mixed with protein, other nucleic acid species, other cellularcomponents and/or any other contaminant. As demonstrated in Example 2below, in some embodiments, the biological sample comprises a mixture ofDNA, protein, other nucleic acid species, other cellular componentsand/or any other contaminant present in approximately the sameproportion as found in vivo. For example, in some embodiments, thecomponents are found in the same proportion as found in an intact cell.In some embodiments, the biological sample has a 260/280 ratio of lessthan 2.0, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0, 0.9, 0.8,0.7, or less than 0.60. In some embodiments, the biological sample has a260/280 ratio of at least 2.0, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3, 1.2,1.1, 1.0, 0.9, 0.8, 0.7, or at least 0.60. Because the methods providedherein allow DNA to be bound to a solid support, other contaminants canbe removed merely by washing the solid support after surface boundtagmentation occurs. The biological sample can comprise, for example, acrude cell lysate or whole cells. For example, a crude cell lysate thatis applied to a solid support in a method set forth herein, need nothave been subjected to one or more of the separation steps that aretraditionally used to isolate nucleic acids from other cellularcomponents. Exemplary separation steps are set forth in Maniatis et al.,Molecular Cloning: A Laboratory Manual, 2d Edition, 1989, and ShortProtocols in Molecular Biology, ed. Ausubel, et al, hereby incorporatedby reference.

Thus, in some embodiments, the biological sample can comprise, forexample, blood, plasma, serum, lymph, mucus, sputum, urine, semen,cerebrospinal fluid, bronchial aspirate, feces, and macerated tissue, ora lysate thereof, or any other biological specimen comprising DNA. Oneadvantage of the methods and compositions presented herein that abiological sample can be added to the flowcell and subsequent lysis andpurification steps can all occur in the flowcell without furthertransfer or handling steps, simply by flowing the necessary reagentsinto the flowcell. Examples 1 and 2 below demonstrate successfulapplication of crude cell lysates to the methods and compositionsprovided herein.

FIGS. 2a and 2b further illustrate the tagmentation reaction accordingto one embodiment. As shown in FIG. 2a , transposomes comprise a dimerof Tn5 with each monomer binding a double stranded molecule, i.e. the MEadaptor. One strand of the ME adaptor is covalently attached to thesurface of a flowcell. Transposomes bind target DNA and generate twonicks in the DNA backbone, 9 bases apart on either strand. Although FIG.2a shows a 9 bp gap between nicks, in other embodiments, the transposomecan generate a gap of 7, 8, 9, 10, 11, or 12 bp between nicks. Only oneof the two strands of each ME adaptor is ligated to the 5′ strand ateach nick position. This strand ‘the transferred strand’ is grafted tothe surface of the flowcell via its 5′ end. The resulting bridge of thesurface tagmentation is redrawn in FIG. 2b to clarify the nature of theresulting bridge.

FIGS. 3a and 3b illustrate an example of the invention put intopractice. Two forms of transposome are assembled on the surface of aflowcell. The first form comprises a P7 transposome in which the‘transfer strand’ of the ME adaptor comprises an extendedoligonucleotide sequence linking the transposome to the surfaceincluding an amplification domain (P7) and a sequencing primer (S2). Thesecond form comprises a P5 transposome in which the ‘transfer strand’ ofthe ME adaptor comprises an extended oligonucleotide sequence linkingthe transposome to the surface including an amplification domain (P5)and a sequencing primer (S1). Addition of DNA to the flowcell results intagmentation and coupling of the DNA to the transposomes. Three types ofbridges result: P5-P5, P7-P7 and P5-P7. Following cluster formation andlinearization (FIG. 3b ), either P5-P5 or P7-P7 clusters are removed(depending on linearization). As shown in FIG. 3b , if linearizationhappens via P5, then only the P5-P7 and P7-P7 bridges remain. P7-P7clusters are not linearized by this reaction and therefore will notsequence. P7-P7 clusters are subsequently removed during Read 2linearization for sequencing.

The method presented herein can further comprise an additional step ofproviding transposome complexes in solution and contacting thesolution-phase transposome complexes with the immobilized fragmentsunder conditions whereby the target DNA is fragmented by the transposomecomplexes solution; thereby obtaining immobilized nucleic acid fragmentshaving one end in solution. In some embodiments, the transposomecomplexes in solution can comprise a second tag, such that the methodgenerates immobilized nucleic acid fragments having a second tag, thesecond tag in solution. The first and second tags can be different orthe same.

In some embodiments, one form of surface bound transposome ispredominantly present on the solid support. For example, in someembodiments, at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,96%, 97%, 98%, or at least 99% of the tags present on said solid supportcomprise the same tag domain. In such embodiments, after an initialtagmentation reaction with surface bound transposomes, at least 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or at least99% of the bridge structures comprise the same tag domain at each end ofthe bridge. A second tagmentation reaction can be performed by addingtransposomes from solution that further fragment the bridges. In someembodiments, most or all of the solution phase transposomes comprise atag domain that differs from the tag domain present on the bridgestructures generated in the first tagmentation reaction. For example, insome embodiments, at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 96%, 97%, 98%, or at least 99% of the tags present in the solutionphase transposomes comprise the a tag domain that differs from the tagdomain present on the bridge structures generated in the firsttagmentation reaction.

FIGS. 4a and 4b illustrate this embodiment. The solid support shown inFIG. 4a comprises only surface bound transposome comprising a singletype of tag sequence (e.g. P5 transposome). In this instance, alltagmented bridges are P5-P5 bridges. A P7 transposome is added fromsolution and tagments into the bridges making all surface boundmolecules P5-P7 templates. The surface bound fragments can besubsequently converted into clusters (see, for example, FIG. 4b ).Furthermore, a pair of clusters will result from each transposome stumpwhich represent the two adjacent fragments in the original intact DNAsample (FIG. 4b ).

Also presented herein are solid supports having a library of tagged DNAfragments immobilized thereon prepared according to the above methods.

Physical Maps of Immobilized Polynucleotide Molecules

Also presented herein are methods of generating a physical map ofimmobilized polynucleotides. The methods can advantageously be exploitedto identify clusters likely to contain linked sequences (i.e., the firstand second portions from the same target polynucleotide molecule). Therelative proximity of any two clusters resulting from an immobilizedpolynucleotide thus provides information useful for alignment ofsequence information obtained from the two clusters. Specifically, thedistance between any two given clusters on a solid surface is positivelycorrelated with the probability that the two clusters are from the sametarget polynucleotide molecule, as described in greater detail in WO2012/025250, which is incorporated herein by reference in its entirety.

As an example, in some embodiments, long dsDNA molecules stretching outover the surface of a flowcell are tagmented in situ, resulting in aline of connected dsDNA bridges across the surface of the flowcell.Further, a physical map of the immobilized DNA can then be generated.The physical map thus correlates the physical relationship of clustersafter immobilized DNA is amplified. Specifically, the physical map isused to calculate the probability that sequence data obtained from anytwo clusters are linked, as described in the incorporated materials ofWO 2012/025250.

In some embodiments, the physical map is generated by imaging the DNA toestablish the location of the immobilized DNA molecules across a solidsurface. In some embodiments, the immobilized DNA is imaged by adding animaging agent to the solid support and detecting a signal from theimaging agent. In some embodiments, the imaging agent is a detectablelabel. Suitable detectable labels, include, but are not limited to,protons, haptens, radionuclides, enzymes, fluorescent labels,chemiluminescent labels, and/or chromogenic agents. For example, in someembodiments, the imaging agent is an intercalating dye ornon-intercalating DNA binding agent. Any suitable intercalating dye ornon-intercalating DNA binding agent as are known in the art can be used,including, but not limited to those set forth in U.S. 2012/0282617,which is incorporated herein by reference in its entirety.

In some embodiments, the immobilized double stranded fragments arefurther fragmented to liberate a free end (see FIG. 4a ) prior tocluster generation (FIG. 4b ). Cleaving bridged structures can beperformed using any suitable methodology as is known in the art, asexemplified by the incorporated materials of WO 2012/025250. Forexample, cleavage can occur by incorporation of a modified nucleotide,such as uracil as described in WO 2012/025250, by incorporation of arestriction endonuclease site, or by applying solution-phase transposomecomplexes to the bridged DNA structures, as described elsewhere herein.

In certain embodiments, a plurality of target DNA molecules is flowedonto a flowcell comprising a plurality of nano-channels, thenano-channel having a plurality of transposome complexes immobilizedthereto. As used herein, the term nano-channel refers to a narrowchannel into which a long linear DNA molecule is flown. In someembodiments, no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 30, 40, 50, 60 70, 80, 90, 100, 200, 300, 400,500, 600, 700, 800, 900 or no more than 1000 individual long strands oftarget DNA are flowed into each nano-channel. In some embodiments theindividual nano-channels are separated by a physical barrier whichprevents individual long strands of target DNA from interacting withmultiple nano-channels. In some embodiments, the solid support comprisesat least 10, 50, 100, 200, 500, 1000, 3000, 5000, 10000, 30000, 50000,80000 or at least 100000 nano-channels. In some embodiments,transposomes bound to the surface of a nano-channel tagment the DNA.Contiguity mapping can then be performed, for example, by following theclusters down the length of one of these channels. In some embodiments,the long strand of target DNA can be at least 0.1 kb, 1 kb, 2 kb, 3 kb,4 kb, 5 kb, 6 kb, 7 kb, 8 kb, 9 kb, 10 kb, 15 kb, 20 kb, 25 kb, 30 kb,35 kb, 40 kb, 45 kb, 50 kb, 55 kb, 60 kb, 65 kb, 70 kb, 75 kb, 80 kb, 85kb, 90 kb, 95 kb, 100 kb, 150 kb, 200 kb, 250 kb, 300 kb, 350 kb, 400kb, 450 kb, 500 kb, 550 kb, 600 kb, 650 kb, 700 kb, 750 kb, 800 kb, 850kb, 900 kb, 950 kb, 1000 kb, 5000 kb, 10000 kb, 20000 kb, 30000 kb, orat least 50000 kb in length. In some embodiments, the long strand oftarget DNA is no more than 0.1 kb, 1 kb, 2 kb, 3 kb, 4 kb, 5 kb, 6 kb, 7kb, 8 kb, 9 kb, 10 kb, 15 kb, 20 kb, 25 kb, 30 kb, 35 kb, 40 kb, 45 kb,50 kb, 55 kb, 60 kb, 65 kb, 70 kb, 75 kb, 80 kb, 85 kb, 90 kb, 95 kb,100 kb, 150 kb, 200 kb, 250 kb, 300 kb, 350 kb, 400 kb, 450 kb, 500 kb,550 kb, 600 kb, 650 kb, 700 kb, 750 kb, 800 kb, 850 kb, 900 kb, 950 kb,or no more than 1000 kb in length. As an example, a flowcell having 1000or more nano-channels with mapped immobilized tagmentation products inthe nano-channels can be used to sequence the genome of an organism withshort ‘positioned’ reads. In some embodiments, mapped immobilizedtagmentation products in the nano-channels can be used resolvehaplotypes. In some embodiments, mapped immobilized tagmentationproducts in the nano-channels can be used to resolve phasing issues.

Amplification and Sequencing Immobilized DNA Fragments

Amplification. The present disclosure further relates to amplificationof the immobilized DNA fragments produced according to the methodsprovided herein. The immobilized DNA fragments produced by surface boundtransposome mediated tagmentation can be amplified according to anysuitable amplification methodology known in the art. In someembodiments, the immobilized DNA fragments are amplified on a solidsupport. In some embodiments, the solid support is the same solidsupport upon which the surface bound tagmentation occurs. In suchembodiments, the methods and compositions provided herein allow samplepreparation to proceed on the same solid support from the initial sampleintroduction step through amplification and optionally through asequencing step.

For example, in some embodiments, the immobilized DNA fragments areamplified using cluster amplification methodologies as exemplified bythe disclosures of U.S. Pat. Nos. 7,985,565 and 7,115,400, the contentsof each of which is incorporated herein by reference in its entirety.The incorporated materials of U.S. Pat. Nos. 7,985,565 and 7,115,400describe methods of solid-phase nucleic acid amplification which allowamplification products to be immobilized on a solid support in order toform arrays comprised of clusters or “colonies” of immobilized nucleicacid molecules. Each cluster or colony on such an array is formed from aplurality of identical immobilized polynucleotide strands and aplurality of identical immobilized complementary polynucleotide strands.The arrays so-formed are generally referred to herein as “clusteredarrays”. The products of solid-phase amplification reactions such asthose described in U.S. Pat. Nos. 7,985,565 and 7,115,400 are so-called“bridged” structures formed by annealing of pairs of immobilizedpolynucleotide strands and immobilized complementary strands, bothstrands being immobilized on the solid support at the 5′ end, preferablyvia a covalent attachment. Cluster amplification methodologies areexamples of methods wherein an immobilized nucleic acid template is usedto produce immobilized amplicons. Other suitable methodologies can alsobe used to produce immobilized amplicons from immobilized DNA fragmentsproduced according to the methods provided herein. For example one ormore clusters or colonies can be formed via solid-phase PCR whether oneor both primers of each pair of amplification primers are immobilized.

In other embodiments, the immobilized DNA fragments are amplified insolution. For example, in some embodiments, the immobilized DNAfragments are cleaved or otherwise liberated from the solid support andamplification primers are then hybridized in solution to the liberatedmolecules. In other embodiments, amplification primers are hybridized tothe immobilized DNA fragments for one or more initial amplificationsteps, followed by subsequent amplification steps in solution. Thus, insome embodiments an immobilized nucleic acid template can be used toproduce solution-phase amplicons.

It will be appreciated that any of the amplification methodologiesdescribed herein or generally known in the art can be utilized withuniversal or target-specific primers to amplify immobilized DNAfragments. Suitable methods for amplification include, but are notlimited to, the polymerase chain reaction (PCR), strand displacementamplification (SDA), transcription mediated amplification (TMA) andnucleic acid sequence based amplification (NASBA), as described in U.S.Pat. No. 8,003,354, which is incorporated herein by reference in itsentirety. The above amplification methods can be employed to amplify oneor more nucleic acids of interest. For example, PCR, including multiplexPCR, SDA, TMA, NASBA and the like can be utilized to amplify immobilizedDNA fragments. In some embodiments, primers directed specifically to thenucleic acid of interest are included in the amplification reaction.

Other suitable methods for amplification of nucleic acids can includeoligonucleotide extension and ligation, rolling circle amplification(RCA) (Lizardi et al., Nat. Genet. 19:225-232 (1998), which isincorporated herein by reference) and oligonucleotide ligation assay(OLA) (See generally U.S. Pat. Nos. 7,582,420, 5,185,243, 5,679,524 and5,573,907; EP 0 320 308 B1; EP 0 336 731 B1; EP 0 439 182 B1; WO90/01069; WO 89/12696; and WO 89/09835, all of which are incorporated byreference) technologies. It will be appreciated that these amplificationmethodologies can be designed to amplify immobilized DNA fragments. Forexample, in some embodiments, the amplification method can includeligation probe amplification or oligonucleotide ligation assay (OLA)reactions that contain primers directed specifically to the nucleic acidof interest. In some embodiments, the amplification method can include aprimer extension-ligation reaction that contains primers directedspecifically to the nucleic acid of interest. As a non-limiting exampleof primer extension and ligation primers that can be specificallydesigned to amplify a nucleic acid of interest, the amplification caninclude primers used for the GoldenGate assay (Illumina, Inc., SanDiego, Calif.) as exemplified by U.S. Pat. Nos. 7,582,420 and 7,611,869,each of which is incorporated herein by reference in its entirety.

Exemplary isothermal amplification methods that can be used in a methodof the present disclosure include, but are not limited to, MultipleDisplacement Amplification (MDA) as exemplified by, for example Dean etal., Proc. Natl. Acad. Sci. USA 99:5261-66 (2002) or isothermal stranddisplacement nucleic acid amplification exemplified by, for example U.S.Pat. No. 6,214,587, each of which is incorporated herein by reference inits entirety. Other non-PCR-based methods that can be used in thepresent disclosure include, for example, strand displacementamplification (SDA) which is described in, for example Walker et al.,Molecular Methods for Virus Detection, Academic Press, Inc., 1995; U.S.Pat. Nos. 5,455,166, and 5,130,238, and Walker et al., Nucl. Acids Res.20:1691-96 (1992) or hyperbranched strand displacement amplificationwhich is described in, for example Lage et al., Genome Research13:294-307 (2003), each of which is incorporated herein by reference inits entirety. Isothermal amplification methods can be used with thestrand-displacing Phi 29 polymerase or Bst DNA polymerase largefragment, 5′→3′ exo⁻ for random primer amplification of genomic DNA. Theuse of these polymerases takes advantage of their high processivity andstrand displacing activity. High processivity allows the polymerases toproduce fragments that are 10-20 kb in length. As set forth above,smaller fragments can be produced under isothermal conditions usingpolymerases having low processivity and strand-displacing activity suchas Klenow polymerase. Additional description of amplification reactions,conditions and components are set forth in detail in the disclosure ofU.S. Pat. No. 7,670,810, which is incorporated herein by reference inits entirety.

Another nucleic acid amplification method that is useful in the presentdisclosure is Tagged PCR which uses a population of two-domain primershaving a constant 5′ region followed by a random 3′ region as described,for example, in Grothues et al. Nucleic Acids Res. 21(5):1321-2 (1993),incorporated herein by reference in its entirety. The first rounds ofamplification are carried out to allow a multitude of initiations onheat denatured DNA based on individual hybridization from therandomly-synthesized 3′ region. Due to the nature of the 3′ region, thesites of initiation are contemplated to be random throughout the genome.Thereafter, the unbound primers can be removed and further replicationcan take place using primers complementary to the constant 5′ region.

Sequencing. The present disclosure further relates to sequencing of theimmobilized DNA fragments produced according to the methods providedherein. The immobilized DNA fragments produced by surface boundtransposome mediated tagmentation can be sequenced according to anysuitable sequencing methodology, such as direct sequencing, includingsequencing by synthesis, sequencing by ligation, sequencing byhybridization, nanopore sequencing and the like. In some embodiments,the immobilized DNA fragments are sequenced on a solid support. In someembodiments, the solid support for sequencing is the same solid supportupon which the surface bound tagmentation occurs. In some embodiments,the solid support for sequencing is the same solid support upon whichthe amplification occurs.

One preferred sequencing methodology is sequencing-by-synthesis (SBS).In SBS, extension of a nucleic acid primer along a nucleic acid template(e.g. a target nucleic acid or amplicon thereof) is monitored todetermine the sequence of nucleotides in the template. The underlyingchemical process can be polymerization (e.g. as catalyzed by apolymerase enzyme). In a particular polymerase-based SBS embodiment,fluorescently labeled nucleotides are added to a primer (therebyextending the primer) in a template dependent fashion such thatdetection of the order and type of nucleotides added to the primer canbe used to determine the sequence of the template.

Flow cells provide a convenient solid support for housing amplified DNAfragments produced by the methods of the present disclosure. One or moreamplified DNA fragments in such a format can be subjected to an SBS orother detection technique that involves repeated delivery of reagents incycles. For example, to initiate a first SBS cycle, one or more labelednucleotides, DNA polymerase, etc., can be flowed into/through a flowcell that houses one or more amplified nucleic acid molecules. Thosesites where primer extension causes a labeled nucleotide to beincorporated can be detected. Optionally, the nucleotides can furtherinclude a reversible termination property that terminates further primerextension once a nucleotide has been added to a primer. For example, anucleotide analog having a reversible terminator moiety can be added toa primer such that subsequent extension cannot occur until a deblockingagent is delivered to remove the moiety. Thus, for embodiments that usereversible termination, a deblocking reagent can be delivered to theflow cell (before or after detection occurs). Washes can be carried outbetween the various delivery steps. The cycle can then be repeated ntimes to extend the primer by n nucleotides, thereby detecting asequence of length n. Exemplary SBS procedures, fluidic systems anddetection platforms that can be readily adapted for use with ampliconsproduced by the methods of the present disclosure are described, forexample, in Bentley et al., Nature 456:53-59 (2008), WO 04/018497; U.S.Pat. No. 7,057,026; WO 91/06678; WO 07/123744; U.S. Pat. Nos. 7,329,492;7,211,414; 7,315,019; 7,405,281, and US 2008/0108082, each of which isincorporated herein by reference.

Other sequencing procedures that use cyclic reactions can be used, suchas pyrosequencing. Pyrosequencing detects the release of inorganicpyrophosphate (PPi) as particular nucleotides are incorporated into anascent nucleic acid strand (Ronaghi, et al., Analytical Biochemistry242(1), 84-9 (1996); Ronaghi, Genome Res. 11(1), 3-11 (2001); Ronaghi etal. Science 281(5375), 363 (1998); U.S. Pat. Nos. 6,210,891; 6,258,568and 6,274,320, each of which is incorporated herein by reference). Inpyrosequencing, released PPi can be detected by being immediatelyconverted to adenosine triphosphate (ATP) by ATP sulfurylase, and thelevel of ATP generated can be detected via luciferase-produced photons.Thus, the sequencing reaction can be monitored via a luminescencedetection system. Excitation radiation sources used for fluorescencebased detection systems are not necessary for pyrosequencing procedures.Useful fluidic systems, detectors and procedures that can be adapted forapplication of pyrosequencing to amplicons produced according to thepresent disclosure are described, for example, in WIPO Pat. App. Ser.No. PCT/US11/57111, US 2005/0191698 A1, U.S. Pat. Nos. 7,595,883, and7,244,559, each of which is incorporated herein by reference.

Some embodiments can utilize methods involving the real-time monitoringof DNA polymerase activity. For example, nucleotide incorporations canbe detected through fluorescence resonance energy transfer (FRET)interactions between a fluorophore-bearing polymerase andγ-phosphate-labeled nucleotides, or with zeromode waveguides (ZMWs).Techniques and reagents for FRET-based sequencing are described, forexample, in Levene et al. Science 299, 682-686 (2003); Lundquist et al.Opt. Lett. 33, 1026-1028 (2008); Korlach et al. Proc. Natl. Acad. Sci.USA 105, 1176-1181 (2008), the disclosures of which are incorporatedherein by reference.

Some SBS embodiments include detection of a proton released uponincorporation of a nucleotide into an extension product. For example,sequencing based on detection of released protons can use an electricaldetector and associated techniques that are commercially available fromIon Torrent (Guilford, Conn., a Life Technologies subsidiary) orsequencing methods and systems described in US 2009/0026082 A1; US2009/0127589 A1; US 2010/0137143 A1; or US 2010/0282617 A1, each ofwhich is incorporated herein by reference. Methods set forth herein foramplifying target nucleic acids using kinetic exclusion can be readilyapplied to substrates used for detecting protons. More specifically,methods set forth herein can be used to produce clonal populations ofamplicons that are used to detect protons.

Another useful sequencing technique is nanopore sequencing (see, forexample, Deamer et al. Trends Biotechnol. 18, 147-151 (2000); Deamer etal. Acc. Chem. Res. 35:817-825 (2002); Li et al. Nat. Mater. 2:611-615(2003), the disclosures of which are incorporated herein by reference).In some nanopore embodiments, the target nucleic acid or individualnucleotides removed from a target nucleic acid pass through a nanopore.As the nucleic acid or nucleotide passes through the nanopore, eachnucleotide type can be identified by measuring fluctuations in theelectrical conductance of the pore. (U.S. Pat. No. 7,001,792; Soni etal. Clin. Chem. 53, 1996-2001 (2007); Healy, Nanomed. 2, 459-481 (2007);Cockroft et al. J. Am. Chem. Soc. 130, 818-820 (2008), the disclosuresof which are incorporated herein by reference).

Exemplary methods for array-based expression and genotyping analysisthat can be applied to detection according to the present disclosure aredescribed in U.S. Pat. Nos. 7,582,420; 6,890,741; 6,913,884 or 6,355,431or US Pat. Pub. Nos. 2005/0053980 A1; 2009/0186349 A1 or US 2005/0181440A1, each of which is incorporated herein by reference.

An advantage of the methods set forth herein is that they provide forrapid and efficient detection of a plurality of target nucleic acid inparallel. Accordingly the present disclosure provides integrated systemscapable of preparing and detecting nucleic acids using techniques knownin the art such as those exemplified above. Thus, an integrated systemof the present disclosure can include fluidic components capable ofdelivering amplification reagents and/or sequencing reagents to one ormore immobilized DNA fragments, the system comprising components such aspumps, valves, reservoirs, fluidic lines and the like. A flow cell canbe configured and/or used in an integrated system for detection oftarget nucleic acids. Exemplary flow cells are described, for example,in US 2010/0111768 A1 and U.S. Ser. No. 13/273,666, each of which isincorporated herein by reference. As exemplified for flow cells, one ormore of the fluidic components of an integrated system can be used foran amplification method and for a detection method. Taking a nucleicacid sequencing embodiment as an example, one or more of the fluidiccomponents of an integrated system can be used for an amplificationmethod set forth herein and for the delivery of sequencing reagents in asequencing method such as those exemplified above. Alternatively, anintegrated system can include separate fluidic systems to carry outamplification methods and to carry out detection methods. Examples ofintegrated sequencing systems that are capable of creating amplifiednucleic acids and also determining the sequence of the nucleic acidsinclude, without limitation, the MiSeq™ platform (Illumina, Inc., SanDiego, Calif.) and devices described in U.S. Ser. No. 13/273,666, whichis incorporated herein by reference.

Solid Supports with Immobilized Transposomes and Methods of Preparation

Other embodiments presented herein include solid supports, such asflowcells, having transposome complexes immobilized thereon. In certainembodiments, the transposome complexes comprise a transposase bound to afirst polynucleotide, the polynucleotide comprising (i) a 3′ portioncomprising a transposon end sequence, and (ii) a first tag comprising afirst tag domain. The density of these surface bound transposomes canvary. For example, in some embodiments, the transposome complexes arepresent on the solid support at a density of at least 10³, 10⁴, 10⁵, orat least 10⁶ complexes per mm².

Also presented herein are methods of generating a flowcell fortagmentation. The methods can comprise, for example, immobilizing aplurality of transposome complexes to a solid support, the transposomecomplexes comprising a transposase bound to a first polynucleotide, thefirst polynucleotide comprising (i) a 3′ portion comprising a transposonend sequence, and (ii) a first tag comprising a first tag domain.

Transposome complexes can be immobilized to a solid support in a varietyof methods, which will be appreciated by one of skill in the art. In oneembodiment, the method comprises providing a solid support having aplurality of first polynucleotides immobilized thereon, and contactingthe solid support with transposase holoenzyme and a secondpolynucleotide, the second polynucleotide comprising a regioncomplementary to the transposon end sequence. In some embodiments, thesecond polynucleotide is hybridized to the immobilized firstpolynucleotide before the transposase holoenzyme is added. In someembodiments, the second polynucleotide and the transposase holoenzymeare provided together. FIG. 5a shows one embodiment of this method forassembling the surface bound transposome complexes. In one method,transposase holoenzyme is added along with the non-transferred strand ofthe ME adaptor to a flowcell containing oligonucleotides comprising fromthe 5′ surface grafted end: a cluster amplification primer (A.pr) andsequencing primer (S.pr) and the ME sequence (FIG. 5a ). Alternatively,the non-transferred ME′ strand can hybridized to the surface grafted MEstrand first and then the transposase added to the flowcell.

In some embodiments, the transposome complexes are assembled in solutionand immobilizing comprises a further step of ligating the firstpolynucleotide to a splint oligonucleotide coupled to the solid support.This embodiment is illustrated in FIG. 5b . In some embodiments, thesplint oligonucleotide can be extended using a polymerase before aligating step occurs.

In some embodiments, transposome dimer is assembled by hybridizing alooped oligonucleotide to an immobilized first polynucleotide. Forexample, a looped oligonucleotide can comprise a first end and a secondend, with the first end being complementary to the transposon endsequence of the first polynucleotide. The second end of the loopedoligonucleotide can be complementary to a second transposon endsequence. The second transposon end sequence can be, for example, partof a solution-phase first polynucleotide. In some embodiments, theimmobilized first polynucleotide and the solution-phase firstpolynucleotide can comprise dissimilar transposon end sequences orcomplements thereof. In some such embodiments, the loopedoligonucleotide comprises sequences complementary to each of thedissimilar transposon end sequences at the first and second ends. Anillustration of this embodiment is shown in FIG. 5c . As shown in FIG.5c , a contiguous adaptor pair is generated by hybridizing twooligonucleotides to the surface bound oligonucleotide. This can beachieved by employing two dissimilar transposon end sequences (ME1 andME2). Addition of transposase holoenzyme reconstitutes an active‘looped’ transposome complex, where only one of the two adaptors of eachtransposome is coupled to the surface FIG. 5 c.

In another embodiment, transposome complexes can be assembled on astandard paired end flow cell with amplification primers immobilizedthereto (e.g. a HiSeq flow cell or MiSeq flow cell sold by Illumina Inc,San Diego, Calif.). This can be accomplished by, for example,hybridization of a ‘splint’ oligonucleotide that anneals to one or bothspecies of surface grafted amplification primer. The splint acts as atemplate to then extend the grafted surface primer with a polymerase anddNTPs to form an oligonucleotide duplex that contains a surfaceamplification primer, a sequencing primer and the transposon endsequences of the transposase. Addition of transposase assembles atransposome of the surface. This embodiment is illustrated in FIG. 5 d.

In any of the embodiments provided herein, transposome complexes may behomodimers, or heterodimers. For example, as illustrated in FIG. 11, ahomodimeric transposome would comprise two P5-ME adaptors at both sitesor alternatively, two P7-ME adaptors. Similarly, a heterodimerictransposome complex would comprise both P5-ME and P7-ME adaptors, asshown in FIG. 11.

Tagmentation Using Transposome Beads

One embodiment presented herein is a population of microparticles havingtransposome complexes immobilized thereto. The use of a solid supportsuch as beads can provide several advantages over solution-basedtagmentation. For example, in standard solution-based tagmentation, itis difficult to control the final fragment size of the tagmentationreaction. Fragment size is a function of the ratio of transposomes tothe amount and size of DNA and to the duration of the reaction. Even ifthese parameters are controlled, size selection fractionation iscommonly required as an additional step to remove excess small fragmentsshorter than the combined paired-read lengths. The methods providedherein avoid those disadvantages. Specifically, bead-immobilizedtransposomes allow for selection of final fragment size as a function ofthe spatial separation of the bound transposomes, independent of thequantity of transposome beads added to the tagmentation reaction. Anadditional limitation of solution-based tagmentation is that it istypically necessary to do some form of purification of the products ofthe tagmentation reaction both before and after PCR amplification. Thistypically necessitates some transfer of reactions from tube to tube. Incontrast, tagmentation products on the bead based transposomes can bewashed and later released for amplification or other downstreamprocessing, thus avoiding the need for sample transfer. For example, inembodiments where transposomes are assembled on paramagnetic beads,purification of the tagmentation reaction products can easily beachieved by immobilizing the beads with a magnets and washing. Thus, insome embodiments, tagmentation and other downstream processing such asPCR amplification can all be performed in a single tube, vessel, dropletor other container. In some embodiments, tagmentation and downstreamprocessing of samples takes place on a microfluidic droplet baseddevice, as exemplified in the disclosure of U.S. application Ser. No.13/670,318, filed on Nov. 6, 2012 entitled “INTEGRATED SEQUENCINGAPPARATUSES AND METHODS OF USE” which is incorporated herein byreference in its entirety. For example, in a microfluidic droplet baseddevice, a droplet containing target nucleic acid, wash buffer or otherreagents may be passed over a surface comprising immobilized transposomecomplexes. Likewise, a droplet comprising beads having transposomesimmobilized thereon may be contacted with target nucleic acid, washbuffer or other reagents in a microfluidic droplet based device.

In some embodiments, the immobilized transposome complexes comprise atransposase bound to a first polynucleotide and a second polynucleotide;wherein the first polynucleotide is immobilized at its 5′ end to thesurface of the microparticle and the second polynucleotide is hybridizedto the 3′ end of the first polynucleotide; and wherein the firstpolynucleotide comprises: (i) a 3′ portion comprising a transposon endsequence, and (ii) a first tag comprising a first tag domain.

FIGS. 9-12 provide an illustration of transposomes assembled on thesurface of paramagnetic beads. FIG. 9 shows a bead surface with twodifferent first polynucleotides immobilized thereto. The firstpolynucleotides that are shown comprise a transposon end sequence (ME).One of the first polynucleotides shown in comprises a tag domaincomprising an amplification primer sequence (P5) and a sequencing primersequence (Read 1). The other polynucleotide shown in FIG. 9 comprises adifferent amplification primer sequence (P7) and a sequencing primersequence (Read 2). The first polynucleotides may also comprise an indextag. The index tag may be unique to the bead, or it may be shared withone or more other beads in the population. A single bead may have only asingle index tag immobilized thereto, or it may have a plurality ofindex tags immobilized thereto.

FIG. 10 shows a second polynucleotide hybridized to each firstpolynucleotide. The second polynucleotide comprises a regioncomplementary to the transposon end sequence of the firstpolynucleotide. In some embodiments, the second polynucleotide is 15 bpin length. In some embodiments, the second polynucleotide can beapproximately 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 bp or more than20 bp in length. In some embodiments, the second polynucleotide isphosphorylated at its 5′ end.

FIG. 11 illustrates assembly of transposomes on the surface of the bead,where transposase enzyme is contacted with the immobilizedoligonucleotides. As shown in FIG. 11, when the transposase is added tothe beads, three types of transposome complexes are formed: a P5:P5, aP7:P7, and a P5:P7 complex (FIG. 11).

When the transposome beads are added to a solution of target DNA in atagmentation buffer, tagmentation takes place, linking the DNA to thesurface of the beads. An immobilized library of tagged DNA fragments isgenerated.

FIG. 12 illustrates an embodiment where successive tagmentation into theDNA results in bridged molecules between transposomes. Where three typesof transposomes are present (as in FIG. 11), three types of bridgecomplexes result: a P5:P5, P7:P7 and P5:P7 complex in a ratio of25:25:50, respectively.

In some embodiments, the length of the bridged fragments can be dictatedby the density of the transposomes on the surface of the bead. Thisdensity is tunable via the amount of oligonucleotide on the surface, theamount of duplex transposon end complexes on the surface and the amountof transposase enzyme added during the transposome assembly. Oncetagmentation is complete, the P5:P7 tagmentation products can beliberated from the surface of the bead using any suitable method. Insome embodiments, the tagmentation products are liberated from the beadsusing an amplification method such as suppression PCR, step-out PCR andthe like. In some embodiments, the tagmentation products are liberatedfrom the beads by cleavage. The cleavage can be, for example, chemical,enzymatic, photochemical or a combination thereof. It will beappreciated that any suitable method for releasing one or moretagmentation products from a solid support can be utilized in themethods provided herein.

DNA can be efficiently contacted with surface bound transposomes usingany suitable method for increasing the probability of contact. Forexample, in some embodiments, precipitation of DNA onto the solidsurface can be utilized to increase contact between the target DNA andthe transposome complexes on the solid surface. Any one of a number ofmethods that are known in the art for contacting DNA with a solidsupport can be utilized, as exemplified by the disclosure of WO2010/115122, which is incorporated by reference in its entirety. As willbe appreciated by one of skill in the art, DNA can be precipitated ontoa solid support by the addition of PEG, ethanol or any one of a varietyof other agents known to precipitate DNA onto surfaces, including, forexample, any one of a number of buffers used in solid phase reversibleimmobilization (SPRI) technology.

In some embodiments, a population of beads bearing immobilizedtransposome complexes can be mixed with an excess of beads that bear notransposomes or oligonucleotides, thereby reducing the likelihood oftagmentation across two or more different beads. Another method toreduce the likelihood of tagmentation across two or more different beadsincludes immobilizing beads so contact between beads is minimized.Immobilization of beads can be accomplished by any of a number oftechniques known in the art, including, for example, immobilizing thebeads via magnetism to the sides of a solid surface such as amicrocentrifuge tube, or any other immobilization technique asexemplified by the incorporated materials of WO 2010/115122.

Methods of Assembling Long Reads Using Barcodes on ImmobilizedTransposomes

Barcode-assisted assembly of DNA fragments enables isolation ofindividual long DNA molecules within a population of DNA molecules andconversion of each molecule into a uniquely barcoded sub-fragmentlibrary. When the entire population of sub-fragmented DNA molecules issequenced, the subfragments can be assembled back into their originallong molecule by reference to the barcodes they contain.

Various methods of barcoding individual DNA molecules are known. Forexample, the ‘dilution method,’ isolates individual long molecules byextreme dilution and aliquoting into separate compartments (e.g., wellsof a plate), such that each well contains only one or just a fewmolecules of DNA. Because each well is physically separate, a librarypreparation can be done in each well with a unique barcode. Thereafterthe contents of the wells are pooled and sequenced. Another methodemploys an emulsion wherein each droplet contains long DNA molecules,library preparation reagents and a barcode unique to each droplet.Another approach uses a large library of indexed looped transposomecomplexes to insert multiple twin barcodes along the length of the DNAwhile preserving the intactness of the molecule. Subsequent cleavagebetween the barcode ‘twins’ yields fragments that can be sequenced andreassembled by matching up the twin barcodes. Each of theabove-mentioned barcoding methods carries with it disadvantages that areovercome by the barcoding methods presented herein.

Presented herein are alternative methods to the above described ways ofisolating and barcoding individual long molecules. The methods presentedherein achieve advantages of physical isolation similar to the emulsionmethod without using emulsions, and at the same time provide acomplexity that is much greater than that provided by the large numberof ‘wells’ used in the dilution method. The unique barcodes of thepresent methods are in some ways analogous to the ‘wells’ of thedilution method except that the number of beads in the bead-based methodcan often be much higher than the number of wells in the dilutionmethod. An additional advantage over the emulsion methods is that in thebead-based method, the barcodes are deterministically distributed (i.e.,one barcode per bead) and not random (i.e. Poisson distributed). Themethods presented herein also achieve the same initial preservation ofmolecule intactness and contiguity but without the need for loopedtransposome complexes as used in some other methods. Additionally, themethods presented herein do not require as large a code space as used insome other methods.

Accordingly, in some embodiments presented herein, barcoding methodcomprise providing a population of microparticles having transposomecomplexes immobilized thereto, the transposome complexes comprising atransposase bound to a first polynucleotide and second polynucleotide.In some embodiments, the first polynucleotide comprises an index domainassociated with the microparticle. In some embodiments, the index domaincan be unique to the microparticle. In some embodiments, the populationof microparticles comprises at least a plurality of index domains. Insome embodiments, the index domain is present on more than onemicroparticle in the population of microparticles. In some embodiments,a microparticle in the population of microparticles comprises more thanone index domain.

The barcoding methods presented herein further comprise applying atarget DNA to the population of microparticles, thereby generatingimmobilized DNA fragments that are tagged with the index domain. DNA canbe efficiently contacted with surface bound transposomes using anysuitable method for increasing the probability of contact as discussedhereinabove, as exemplified by the incorporated materials of WO2010/115122.

The methods can be performed using any one of a variety of knownformats, for example, with a combination of tagmentation reagents and abead array for the library preparation, followed by an indexedsequencing run and bespoke data analysis. Any other suitable method thatmaintains beads in static separation from one another can be used forsurface tagmentation and indexing of samples. For example, physicalconfigurations such as wells or small depressions in the substrate thatcan retain the beads, such that a microsphere can rest in the well, orthe use of other forces (magnetic or compressive), or chemically alteredor active sites, such as chemically functionalized sites,electrostatically altered sites, hydrophobically and/or hydrophilicallyfunctionalized sites, or spots of adhesive.

In some embodiments, the microspheres are non-covalently associated inthe wells, although the wells may additionally be chemicallyfunctionalized as is generally described below, cross-linking agents maybe used, or a physical barrier may be used, e.g., a film or membraneover the beads.

In certain embodiments, the surface of the substrate is modified tocontain chemically modified sites that can be used to attach, eithercovalently or non-covalently, the microspheres of the invention to thediscrete sites or locations on the substrate. “Chemically modifiedsites” in this context includes, but is not limited to, the addition ofa pattern of chemical functional groups including amino groups, carboxygroups, oxo groups and thiol groups, that can be used to covalentlyattach microspheres, which generally also contain corresponding reactivefunctional groups; the addition of a pattern of adhesive that can beused to bind the microspheres (either by prior chemicalfunctionalization for the addition of the adhesive or direct addition ofthe adhesive); the addition of a pattern of charged groups (similar tothe chemical functionalities) for the electrostatic attachment of themicrospheres, e.g., when the microspheres comprise charged groupsopposite to the sites; the addition of a pattern of chemical functionalgroups that renders the sites differentially hydrophobic or hydrophilic,such that the addition of similarly hydrophobic or hydrophilicmicrospheres under suitable experimental conditions will result inassociation of the microspheres to the sites on the basis ofhydroaffinity. For example, the use of hydrophobic sites withhydrophobic beads, in an aqueous system, drives the association of thebeads preferentially onto the sites. As outlined above, “pattern” inthis sense includes the use of a uniform treatment of the surface toallow attachment of the beads at discrete sites, as well as treatment ofthe surface resulting in discrete sites. As will be appreciated by thosein the art, this may be accomplished in a variety of ways.

In certain embodiments, a multitude of beads comprising surface boundtransposomes are generated, wherein each bead contains many transposomesbut all transposomes on any given bead all contain the same barcode. Thegeneration of a population of monoclonal barcoded transposomeoligonucleotides on beads can be performed according to any one of anumber of techniques as is known in the art, as exemplified by thedisclosure of U.S. Pat. No. 5,604,097, which is incorporated byreference in its entirety.

FIG. 13 illustrates one embodiment, where a surface bound transposomecontains long oligonucleotides attached to the surface via their 5′ end.As set forth in FIG. 13, the 3′ end of the oligonucleotide comprises theMosaic End (METS) sequences of the Tn5 transposase enzyme. Upstream ofthis sequence (closer to the 5′ end) is a barcode sequence of typically6-8 bases in length. Further upstream is a primer sequence.Additionally, the oligonucleotide can further comprise a cleavage siteto enable the oligonucleotide to be cleaved off the surface; itspresence in the oligonucleotide is optional to the overall method. Asecond short oligonucleotide (the non-transferred strand, MENTS) ishybridized to the METS sequence at the 3′ end of the long surfacegrafted oligonucleotide. Finally, a transposase dimer is assembled atthe 3′ end of the oligonucleotides to form a functional transposome.

FIG. 14 illustrates barcoding on beads in an array of wells. As shown inFIG. 14, when long molecules of dsDNA are added to an array ofbead-immobilized transposomes, a given molecule encounters a bead andgets tagmented many times by the transposomes on the bead. Each fragmentbecomes immobilized to the bead and tagged with the barcode associatedwith that bead. In the particular embodiment shown in FIG. 14, thephysical separation of beads in the array chip prevents a DNA moleculefrom reaching between two beads. In other embodiments, the beads are inclose contact and one or more DNA molecules may stretch between two ormore beads. In some embodiments, more than one DNA molecule can betagmented per bead. The probability of two alleles being tagmented ontothe same bead is low and is a function of the concentration of the DNAadded, the number of beads and the number of barcodes. For example, toavoid two alleles occurring in the same well, 0.1× haplome equivalents(50,000 genomes equivalents) would need to be loaded to 1 million beadseach with a unique barcode.

FIG. 15 illustrates transfer of barcoded tagged molecules to asequencing reaction. As shown in FIG. 15, once the tagmentation iscomplete the DNA is transferred from the bead surface to solution sothat individual fragments can be pooled and prepared for sequencing.Sequencing and assembly by reference to the barcodes enables thesequence of the original long tagmented DNA molecules to be re-created,thus enabling long or pseudo-long reads and phasing of SNPs.

Release of the barcoded surface tagmented fragments to the solutions canbe achieved using any suitable methodology as is known in the art. Forexample, in some embodiments, the tagmented molecules can be cleaved offthe surface of the beads via a cleavage moiety present at the 5′ end ofthe surface bound oligonucleotides (see FIG. 13). The cleavage moietycan be any moiety suitable for cleavage of a nucleic acid strand from asolid support. Examples of methods that utilize a cleavage moietyinclude, but are not limited to, restriction endonuclease cleavage,chemical cleavage, RNase cleavage, photochemical cleavage, and the like,including those cleavage methods and cleavage moieties set forth in WO2006/064199, which is incorporated by reference in its entirety.

Cleavage using a cleavage moiety yields a molecule having the followingformat:

5′-Primer-Barcode-ME-Insert-ME-Barcode-Primer-3′

The “Primer” regions can be used as hybridization points to hybridizePCR step-out primers that enable additional sequences to be added suchas amplification and sequencing primers. For example, amplificationprimers P5 and P7 can be added. Once added, suppression PCR can be used,for example, to enrich for molecules that have P5 adaptors on one endand P7 on the other.

In some embodiments, amplification can be performed directly off thebeads with step-out primers that add P5 and P7 adaptor sequences bysuppression PCR. In another embodiment, each bead can have two types ofsurface grafted oligonucleotides where the primer sequence (as in FIG.13) is either P5-Read1 sequencing primer or P7-Read 2 sequencing primer.This will result in mixed P5-P7 transposomes. These can either becleaved off the beads and followed by suppression PCR to enrich theP5/P7 molecules or amplified directly off the beads, as described above.

In some embodiments, a single transposome type (e.g. P5-Read 1-barcode)may be present on the surface of the bead. Once surface tagmentation iscomplete, a second transposome bearing a different amplification and/orsequencing primer can be added in solution to cleave the bridgedmolecules. This yields all molecules with the same adaptor format thatcan either be cleaved or amplified off the bead surface. An additionalsample-specific barcode could be added to the solution transposome suchthat multiple samples can be pooled by the method. FIG. 16 is anillustration of this embodiment. As shown in FIG. 16, solution-phasetransposomes bearing a P7 amplification primer sequence are added to abead with immobilized bridged tagmentation products. The immobilizedfragments are tagged with a polynucleotide sequence comprising a P5amplification primer sequence and an barcode index tag (i9) that isunique to the bead. As shown in FIG. 16, after the second tagmentationreaction, each fragment has a free end bearing a P7 primer sequence andan immobilized end bearing a P5 primer sequence.

Example 1 Surface Tagmentation on a Flowcell

This example describes an experiment confirming the embodimentillustrated in FIGS. 4a and 4b (surface tagmentation followed bysolution tagmentation).

An experiment on an 8 lane flowcell was carried out using a list ofconditions and controls as shown in FIGS. 6a and 6b . Lane 6 indicatesthe complete end to end exposition of the method: unfragmented E. coligenomic DNA was added to a flowcell where upon it was tagmented by thesurface bound transposomes. Next heat was applied to the flowcell toselectively dehybridize the naked ME sequences thus abolishing them as atarget for a second tagmentation reaction when transposome was nextadded from solution. Following the second tagmentation reaction,clusters were generated and ‘paired-end’ sequenced (2×36 base reads) wasperformed. Sequencing metrics are given in slide 7 which show that inlane 6, 73.14% of clusters passed filters and 74.69 of these aligned.This provides enough data to yield a gap size plot of the inserts and anestimation of library diversity (see FIG. 8).

Other lanes included controls which are listed below:

Lane 1 comprises PhiX DNA as a positive control to ensure everything hasbeen pumping correctly and cluster generation and sequencing works asexpected.

Lane 2 is another control lane and illustrates tagmentation into surfacebound transposons in the absence of target DNA. The flowcell (FC)comprises a standard paired end FC onto which an oligonucleotidecontaining the tagmentation primer sequence and ME′ sequence(non-transferred ME′ strand) was hybridized to the P7 surfaceoligonucleotide. This oligonucleotide was added at a saturatingconcentration. First extension resulted in a double stranded transposonwith ME ends. A P5 transposome was assembled in solution and flowed ontothe FC (6.25 nM/lane). The P5 transposome tagments the double strandedsurface bound transposons. The tagmentation products are subsequentlyconverted into clusters.

Lane 3 illustrates tagmentation into surface bound transposons in theabsence of target DNA, only in this instance the FC has been heated to75° C. in order to convert the ds surface bound transposons into singlestranded oligonucleotides prior to the addition of the P5 Transposomefrom solution in order to prevent tagmentation into these constructs, asthis was interfering with the tagmentation of the target DNA.

Lane 4 illustrates the addition of a surface bound transposome to thelane 3 conditions. In this lane an oligonucleotide containing thetagmentation primer sequence and ME′ sequence was hybridized to the P7surface oligonucleotide. First extension results in a double strandedtransposon with ME ends. Following this a P7 transposome was assembledon the surface of the FC by adding Tn5 enzyme to the lane at 50×concentration and incubating at 30° C. for 30 minutes. The FC was thenheated to 75° C. prior to adding P5 Transposome from solution.

Lane 5 comprises the same conditions as lane 4, only in this caseinstead of adding P5 Transposome from solution, an E. coli 900 bplibrary (with P5/P7 ends) was added to determine whether the P7 surfacebound transposome remains active after the heating step.

Lane 6 illustrates an example of the invention put into practice. Inthis instance the FC comprises of a standard paired end FC onto which anoligonucleotide containing the tagmentation primer sequence and ME′sequence was hybridized to the P7 surface oligonucleotide. Firstextension results in double stranded transposons with ME ends. P7transposomes are assembled on the surface of the FC by adding Tn5 enzymeto the lane at 50× concentration and incubating at 30° C. for 30minutes. Target DNA (300 ng of unfragmented E. coli genomic DNA) wasadded onto the FC lane and an incubation step of 15 min at 55° C. wascarried out in order for tagmentation to take place. The P7 surfacebound transposome was washed off using PBI (Qiagen) and the FC was thenheated to 75° C. prior to adding P5 transposome from solution. Followingaddition of P5 transposome from solution and an incubation step of 15min at 55° C., a stand displacement extension reaction was carried outin order to fill in the 9-bp gaps generated in the DNA backbone by thetransposition reaction. The stand displacement extension reactioncomprises of the addition of a Bst and dNTP mix and incubation at 65° C.for 5 min. The P5 transposome was washed off in the final step. At thispoint all surface bound molecules should be P5-P7 templates and cantherefore be converted into clusters.

Lane 7 comprises of the same conditions as lane 6, only in this instancethe heat step has been left out in order to highlight the effect of heaton the cluster number and % align.

Lane 8 comprises a negative control where the P7 transposome has beenassembled on the surface at 50× concentration in the presence of asaturating concentration of ds surface bound transposons, however, notarget DNA has been added. This allows an assessment of whether thesurface bound P7 transposome tagments into its neighboring ds surfacebound transposons.

Example 2 Surface Bound Sample Preparation from an E. coli Scrape

An E. coli sample (5 mm by 2 mm scrape from a lawn on an agar plate) wasscraped and resuspended in a tube containing water and glass beads. Thesuspended cells and beads were mixed using a vortex mixer to break openthe cells and then centrifuged to pellet cellular debris. Thesupernatant (containing the cell lysate, including proteins and nucleicacids) was removed and added to a Genome Analyzer flowcell (Illumina,Inc., San Diego, Calif.) having immobilized transposomes according tothe protocol described in Example 1.

Cluster generation was performed on the flowcell using a Cluster Stationsample preparation device (Illumina, Inc., San Diego, Calif.). Aftercluster generation, a paired-end sequencing run was performed with readsof 36 bases in each direction.

For Read 1, 58.99% of clusters passed filters and 92.16 of thesealigned. For Read 2, 58.99% of clusters passed filters and 55.08 ofthese aligned. These data confirm that unpurified cell lysates can beadded directly to a flowcell having immobilized transposomes withsurprisingly robust sequencing results.

Example 3

This example describes methods to avoid tagmentation of surface-boundoligonucleotide duplexes when solution phase transposomes are added to aflowcell.

One method for assembling transposomes on the surface of a flow cell isto take a standard paired end flow cell, hybridize a ‘splint’oligonucleotide against the P5 and/or P7 surface graftedoligonucleotides forming an extendable overhang that can be extendedwith a polymerase to make a duplex containing a double stranded MEsequence. At this stage transposase enzyme can be added to form afunctional surface bound transposome (FIG. 5d ). If only a portion ofthe duplexes form a transposome, remaining ‘naked’ ME duplexes maysubsequently become targets for tagmentation by either nearbysurface-bound transposomes or transposomes added from solution.Furthermore, fully assembled surface transposomes contain dsDNA portionsupstream of the ME sequences that can also become targets fortagmentation by nearby surface-bound transposomes or transposomes addedfrom solution. This undesired tagmentation manifests itself in areduction of the percentage of clusters passing purity filters thatalign to the target genome.

An example of this effect can be seen by comparing lanes 4 and 5 versuslanes 6 and 7 in FIG. 18b . In lanes 6 and 7 transposomes were assembledas described above with the long splint oligonucleotides that, afterextension and transposome assembly, produced surface bound duplexes thathave at least 50 double stranded bases. Upon use in a surfacetagmentation reaction (FIG. 18a ) and subsequent sequencing, only 22.59and 15.52% of clusters aligned to the target E. coli respectively (FIG.18b ).

To avoid producing a population of clusters that contain sequences thatdo not align to the target genomic DNA, transposome assembly was done asindicated in FIG. 17. A ‘splint’ oligonucleotide was first hybridizedagainst the P5 and/or P7 surface grafted oligonucleotides forming anextendable overhang that could be extended with a polymerase to make aduplex containing a double stranded ME sequence. Next, the splintoligonucleotide was removed by de-annealing and washing away, and thenwas replaced by hybridizing a shorter oligonucleotide as little as 12bases long but preferably 16 bases long to the 3′ end of the surfaceattached ME oligonucleotide. Transposase was added to assemble atransposome that did not contain any exposed dsDNA. Any ‘naked’ duplexesthat did not contain a bound transposase were removed by incubating theflow cell at 60° C. and washing under flow conditions to selectivelyde-anneal and remove the short duplex DNA.

The beneficial effect of this approach to assembling transposomes can beseen in Lanes 4 and 5 where the surface bound transposomes wereassembled by this method and used in a surface tagmentation reaction(FIG. 18a ). The percentage of clusters that aligned to E. coliincreases from 22.59 and 15.52% for lane 6 and 7 respectively, to 96.47and 96.41 for lanes 4 and 5 respectively (FIG. 18b ).

Throughout this application various publications, patents and/or patentapplications have been referenced. The disclosure of these publicationsin their entireties is hereby incorporated by reference in thisapplication.

The term comprising is intended herein to be open-ended, including notonly the recited elements, but further encompassing any additionalelements.

A number of embodiments have been described. Nevertheless, it will beunderstood that various modifications may be made. Accordingly, otherembodiments are within the scope of the following claims.

What is claimed is:
 1. A solid support having transposome complexesimmobilized thereon, wherein each transposome complex comprises ahomodimer of a transposase non-covalently bound to a firstpolynucleotide of a double-stranded nucleic acid comprising the firstpolynucleotide and a second polynucleotide, wherein the firstpolynucleotide comprises: (i) a 3′ portion comprising a transposon endsequence, and (ii) a first tag comprising a tag domain; wherein thesecond polynucleotide comprises a region complementary to the transposonend sequence; wherein the transposome complexes comprise a first subsetof homodimers, the first subset comprising a first sequence of the firstpolynucleotide, and a second subset of homodimers, the second subsetcomprising a second sequence of the first polynucleotide, wherein thesecond sequence is different than the first sequence; and thetransposome complexes are bound to an immobilized oligonucleotide. 2.The solid support of claim 1, wherein the tag domain comprises asequence region for cluster amplification or priming a sequencingreaction.
 3. The solid support of claim 1, wherein the first sequence orthe second sequence are part of the tag domain.
 4. The solid support ofclaim 1, wherein the transposome complex comprises a hyperactive Tn5transposase.
 5. The solid support of claim 1, wherein the solid supportcomprises microparticles, a patterned surface, wells, a surface of aflow cell, or a population of microparticles distributed on a solidsurface of a flow cell.
 6. The solid support of claim 1, wherein thefirst subset of the homodimers is immobilized to a first plurality ofbeads and the second subset of the homodimers is immobilized to a secondplurality of beads.
 7. The solid support of claim 6, wherein thetransposome complexes are immobilized to the solid support via the firstpolynucleotide.
 8. The solid support of claim 1, wherein the solidsupport is a population of microparticles, and the first polynucleotideis immobilized at its 5′ end to the surface of the microparticle and thesecond polynucleotide is hybridized to the 3′ end of the firstpolynucleotide.
 9. The population of microparticles of claim 8, whereineach microparticle comprises a plurality of said transposome complexes.10. The population of microparticles of claim 8, wherein the firstpolynucleotide further comprises an index domain.
 11. The population ofmicroparticles of claim 10, wherein the population comprises a pluralityof index domains on the first polynucleotides.
 12. The population ofmicroparticles of claim 8, wherein the microparticles are beads.
 13. Thepopulation of microparticles of claim 12, wherein the beads areparamagnetic.
 14. The solid support of claim 1, wherein the solidsupport is a surface of a flow cell or a population of microparticlesdistributed on a solid surface of a flow cell.
 15. The solid support ofclaim 1, wherein the first sequence and the second sequence compriseindex tags.
 16. The solid support of claim 1, wherein the first sequencecomprises a first type of amplification domain and the second sequencecomprises a second type of amplification domain.
 17. The solid supportof claim 1, wherein the first polynucleotide is longer than the secondpolynucleotide such that the first polynucleotide is partiallysingle-stranded.
 18. A method of generating a flow cell comprising:immobilizing a plurality of transposome complexes to a solid support,wherein the solid support comprises a surface of a flow cell ormicroparticles distributed on a surface of the flow cell; wherein eachtransposome complex comprises a transposase bound to a firstpolynucleotide and a second polynucleotide; wherein the firstpolynucleotide comprises: (i) a 3′ portion comprising a transposon endsequence, and (ii) a first tag comprising a tag domain; and the secondpolynucleotide comprises a region complementary to the transposon endsequence; and wherein the transposome complexes comprise homodimers, thehomodimers comprising a first plurality of homodimers and a secondplurality of homodimers, wherein the first polynucleotide of the firstplurality of homodimers comprises a first sequence and the firstpolynucleotide of the second plurality of homodimers comprises a secondsequence different than the first sequence.
 19. The method of claim 18,wherein the immobilizing comprises: providing a solid support having aplurality of the first polynucleotides immobilized thereon, andcontacting the solid support with a transposase holoenzyme and thesecond polynucleotide.
 20. The method of claim 19, wherein thecontacting comprises: hybridizing the second polynucleotide to the firstpolynucleotide immobilized to the solid support and then contacting thesolid support with the transposase holoenzyme; or contacting thetransposase holoenzyme and the second polynucleotide with the solidsupport concurrently.
 21. The method of claim 18, wherein theimmobilizing comprises: providing a solid support having amplificationprimers coupled thereto; hybridizing the second polynucleotide to one ofsaid amplification primers, wherein the second oligonucleotide comprisesa region complementary to the first tag; extending the amplificationprimer using a polymerase to generate a duplex comprising the firstpolynucleotide hybridized to the second polynucleotide, the firstpolynucleotide immobilized directly to the solid support; and contactingthe solid support with a transposase holoenzyme, thereby assembling atransposome complex on the solid support.
 22. The method of claim 18,wherein the tag domain comprises a region for cluster amplification or aregion for priming a sequencing reaction.
 23. A method of generating alibrary of tagged DNA fragments for index-directed assembly into alonger sequence read comprising: applying a target DNA to the solidsupport of claim 1; wherein the solid support is a population ofmicroparticles; and the first polynucleotide comprises an index domain;thereby generating immobilized DNA fragments that are tagged with theindex domain.
 24. The method of claim 23, wherein the firstpolynucleotide is immobilized at its 5′ end to the surface of themicroparticle, the second polynucleotide is hybridized to the 3′ end ofthe first polynucleotide, the population of microparticles comprises aplurality of index domains, and the first polynucleotides on anindividual microparticle share the same index domain.
 25. The method ofclaim 23, wherein the first polynucleotide comprises a cleavage domainfor liberating said first polynucleotide from said microparticle, aregion for cluster amplification, or a region for priming a sequencingreaction.
 26. The method of claim 23, wherein the population ofmicroparticles is distributed on a solid surface, optionally wherein thesolid surface comprises an array of wells, optionally wherein aplurality of said wells comprise one microparticle per well.
 27. Themethod of claim 23, further comprising: (a) performing a sequencingreaction to determine the sequence of the index domain and at least aportion of the tagged DNA fragment, optionally further comprisingassembling DNA sequences that share common index domains, therebygenerating a longer sequence read comprising a plurality ofsub-fragments, or (b) determining the phasing SNPs in said sequenceread.
 28. A method of sequencing a plurality of target DNA moleculescomprising: applying a plurality of target DNA molecules to the solidsupport of claim 1 under conditions whereby the target DNA molecules arefragmented by the transposome complexes, thereby producing animmobilized library of double-stranded fragments, wherein a firstportion of each target DNA molecule is attached to the solid support ata first location on the solid support and a second portion of eachtarget DNA molecule is attached to the solid support at a secondlocation on the solid support; mapping the immobilized library ofdouble-stranded fragments to generate a set of locations that is linkedby each target DNA molecule; determining the sequences of the first andsecond portions of the target DNA molecules; and correlating the set oflocations to determine which first and second portions are linked by thetarget DNA molecules and to determine the sequence of the plurality oftarget DNA molecules.
 29. The method of claim 28, wherein determiningcomprises cleaving the immobilized double-stranded fragments to liberatea free end, optionally by cleaving a cleavable site or by contacting theimmobilized double-stranded fragments with a solution-phase transposasecomplex, wherein the cleavable site optionally comprises a modifiednucleotide or restriction enzyme site.
 30. The method of claim 28,wherein mapping comprises generating a physical map of the immobilizeddouble-stranded fragments, wherein the generating optionally comprisesimaging the DNA to establish the location of the immobilized DNAmolecules on the solid surface, wherein the imaging optionally comprisesadding an imaging agent, a detectable label, or an intercalating dye tothe solid support and detecting a signal from the imaging agent.
 31. Themethod of claim 28, wherein the solid support comprises a flow cell,optionally wherein the flow cell comprises a nano-channel.